This is how I go about it:
HOW TO USE THE LENSALIGN SET-UP TO ALIGN YOUR CAMERA’S AUTO FOCUS FOR A PARTICULAR LENS
1) Set the camera to shoot monochrome images
2) Set the camera to either Manual Mode or Aperture Priority Mode
3) Set the camera to use only a single auto focus point in the center of the viewfinder
4) Set the camera to shoot only a single image when the shutter is pressed
5) Turn the camera’s Fine Tune setting to “Off” for your test shot
6) Set the aperture to F/8 for your test shot and in order to see if the LensAlign target is centered
7) Set the camera to shoot Large, Fine, JPEG images
8) Use a tripod and a cable release
9) Set the front of the camera body (not the front of the lens) at the correct distance from the front of the LensAlign target (actually, it is measured from the "sensor plane", which is usually
marked on top of the camera body. The D800 has it in white, next to the top LCD window as an
oblong circle with a line through it).
10) Make sure the LensAlign target is perfectly centered (view a test shot on your computer screen
to make sure-see 12, below)
11) Make sure the background, behind the LensAlign is black, or dark
12) Shoot a test shot to determine if the LensAlign target is correctly centered
13) If satisfied the LensAlign target is perfectly centered, change your aperture to its lowest number (i.e.; F/1.8 or 2.8, etc.- as long as your highlights are visible in the image; and not blown out)
14) Turn the camera’s Fine Tune setting back to “On” for your Fine Tune adjustment shots
15) Defocus the lens by manually moving the lens focus all the way to one side. Half-press the shutter to reacquire autofocus. Shoot an image; and look at it on the computer screen for accuracy of the “O” being in focus. The smaller numbers on the ruler give a better evaluation.
16) If necessary, go into the camera’s Fine Tune menu and adjust the focus point at various “+” or “-“settings. Defocus the lens, again; and re-shoot at those various new settings. After each test shot, re-evaluate the sharpness of the “O” on the LensAlign ruler. Keep adjusting your Fine Tune settings until the “O” on the LensAlign ruler is its sharpest.
17) Once properly adjusted, leave the camera’s Fine Tune setting “On”.
18) Go out; and take a few "field" shots; and evaluate them accuracy on your computer.